[1] "/home/rstudio/workshop-r-2022"An Advanced Introduction to
Kazuharu Yanagimoto
January 13, 2023
Project Based Workflow
Q. Why Don’t Your Codes Work on My Computer?
A. Conflicts in Path or Package Version
A. You don’t use here and renv
R Project
Have you ever click this button?
You should ALWAYS use R Project!
Why Do We Need to Use R Project?
Path Manager
Package Manager
Always Use here for Paths
The function here::here() treats the proejct directory as the root directory.
You should always specify the path by here::here()
It works in Windows, Mac, Linux (of course, in a Docker environment)
Remember…
If the first line of your R script is
setwd("C:\Users\jenny\path\that\only\I\have")I* will come into your office and SET YOUR COMPPUTER ON FIRE 🔥.
–Jenny Bryan
renv Is Smarter than Us
- Init the environment with
renv::init(). It createsrenv/andrenv.lockfile - At some point, you can record your package and its version information with
renv::snapshot() - Your collaborater can install the packages just by
renv::restore()
renv.lock
{
"R": {
"Version": "4.2.2",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://packagemanager.posit.co/cran/latest"
}
]
},
"Packages": {
"DBI": {
"Package": "DBI",
"Version": "1.1.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "b2866e62bab9378c3cc9476a1954226b",
"Requirements": []
},
"MASS": {
"Package": "MASS",
"Version": "7.3-58.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "762e1804143a332333c054759f89a706",
"Requirements": []
},
"Matrix": {
"Package": "Matrix",
"Version": "1.5-1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "539dc0c0c05636812f1080f473d2c177",
"Requirements": [
"lattice"
]
},
"R6": {
"Package": "R6",
"Version": "2.5.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "470851b6d5d0ac559e9d01bb352b4021",
"Requirements": []
},
"RColorBrewer": {
"Package": "RColorBrewer",
"Version": "1.1-3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "45f0398006e83a5b10b72a90663d8d8c",
"Requirements": []
},
"askpass": {
"Package": "askpass",
"Version": "1.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "e8a22846fff485f0be3770c2da758713",
"Requirements": [
"sys"
]
},
"assertthat": {
"Package": "assertthat",
"Version": "0.2.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "50c838a310445e954bc13f26f26a6ecf",
"Requirements": []
},
"backports": {
"Package": "backports",
"Version": "1.4.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "c39fbec8a30d23e721980b8afb31984c",
"Requirements": []
},
"base64enc": {
"Package": "base64enc",
"Version": "0.1-3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "543776ae6848fde2f48ff3816d0628bc",
"Requirements": []
},
"bit": {
"Package": "bit",
"Version": "4.0.5",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "d242abec29412ce988848d0294b208fd",
"Requirements": []
},
"bit64": {
"Package": "bit64",
"Version": "4.0.5",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "9fe98599ca456d6552421db0d6772d8f",
"Requirements": [
"bit"
]
},
"blob": {
"Package": "blob",
"Version": "1.2.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "10d231579bc9c06ab1c320618808d4ff",
"Requirements": [
"rlang",
"vctrs"
]
},
"broom": {
"Package": "broom",
"Version": "1.0.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "1773f8d5102f9853ecd18a0d13d460fd",
"Requirements": [
"backports",
"dplyr",
"ellipsis",
"generics",
"glue",
"purrr",
"rlang",
"stringr",
"tibble",
"tidyr"
]
},
"bslib": {
"Package": "bslib",
"Version": "0.4.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "a7fbf03946ad741129dc81098722fca1",
"Requirements": [
"base64enc",
"cachem",
"htmltools",
"jquerylib",
"jsonlite",
"memoise",
"mime",
"rlang",
"sass"
]
},
"cachem": {
"Package": "cachem",
"Version": "1.0.6",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "648c5b3d71e6a37e3043617489a0a0e9",
"Requirements": [
"fastmap",
"rlang"
]
},
"callr": {
"Package": "callr",
"Version": "3.7.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9b2191ede20fa29828139b9900922e51",
"Requirements": [
"R6",
"processx"
]
},
"cellranger": {
"Package": "cellranger",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "f61dbaec772ccd2e17705c1e872e9e7c",
"Requirements": [
"rematch",
"tibble"
]
},
"cli": {
"Package": "cli",
"Version": "3.5.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "eb9fc121ad9a1075c471107ef185be46",
"Requirements": []
},
"clipr": {
"Package": "clipr",
"Version": "0.8.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "3f038e5ac7f41d4ac41ce658c85e3042",
"Requirements": []
},
"colorspace": {
"Package": "colorspace",
"Version": "2.0-3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "bb4341986bc8b914f0f0acf2e4a3f2f7",
"Requirements": []
},
"cpp11": {
"Package": "cpp11",
"Version": "0.4.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "ed588261931ee3be2c700d22e94a29ab",
"Requirements": []
},
"crayon": {
"Package": "crayon",
"Version": "1.5.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "e8a1e41acf02548751f45c718d55aa6a",
"Requirements": []
},
"curl": {
"Package": "curl",
"Version": "4.3.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "0eb86baa62f06e8855258fa5a8048667",
"Requirements": []
},
"data.table": {
"Package": "data.table",
"Version": "1.14.6",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "aecef50008ea7b57c76f1cb5c127fb02",
"Requirements": []
},
"dbplyr": {
"Package": "dbplyr",
"Version": "2.2.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "f6c7eb9617e4d2a86bb7182fff99c805",
"Requirements": [
"DBI",
"R6",
"assertthat",
"blob",
"cli",
"dplyr",
"glue",
"lifecycle",
"magrittr",
"pillar",
"purrr",
"rlang",
"tibble",
"tidyselect",
"vctrs",
"withr"
]
},
"digest": {
"Package": "digest",
"Version": "0.6.31",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "8b708f296afd9ae69f450f9640be8990",
"Requirements": []
},
"dplyr": {
"Package": "dplyr",
"Version": "1.0.10",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "539412282059f7f0c07295723d23f987",
"Requirements": [
"R6",
"generics",
"glue",
"lifecycle",
"magrittr",
"pillar",
"rlang",
"tibble",
"tidyselect",
"vctrs"
]
},
"dtplyr": {
"Package": "dtplyr",
"Version": "1.2.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "c5f8828a0b459a703db190b001ad4818",
"Requirements": [
"crayon",
"data.table",
"dplyr",
"ellipsis",
"glue",
"lifecycle",
"rlang",
"tibble",
"tidyselect",
"vctrs"
]
},
"ellipsis": {
"Package": "ellipsis",
"Version": "0.3.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "bb0eec2fe32e88d9e2836c2f73ea2077",
"Requirements": [
"rlang"
]
},
"evaluate": {
"Package": "evaluate",
"Version": "0.19",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "5aac3cd0a3ccb1a738941796b28c26fe",
"Requirements": []
},
"fansi": {
"Package": "fansi",
"Version": "1.0.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "83a8afdbe71839506baa9f90eebad7ec",
"Requirements": []
},
"farver": {
"Package": "farver",
"Version": "2.1.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "8106d78941f34855c440ddb946b8f7a5",
"Requirements": []
},
"fastmap": {
"Package": "fastmap",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "77bd60a6157420d4ffa93b27cf6a58b8",
"Requirements": []
},
"forcats": {
"Package": "forcats",
"Version": "0.5.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "9d95bc88206321cd1bc98480ecfd74bb",
"Requirements": [
"cli",
"ellipsis",
"glue",
"lifecycle",
"magrittr",
"rlang",
"tibble",
"withr"
]
},
"fs": {
"Package": "fs",
"Version": "1.5.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "7c89603d81793f0d5486d91ab1fc6f1d",
"Requirements": []
},
"gargle": {
"Package": "gargle",
"Version": "1.2.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "cca71329ad88e21267f09255d3f008c2",
"Requirements": [
"cli",
"fs",
"glue",
"httr",
"jsonlite",
"rappdirs",
"rlang",
"rstudioapi",
"withr"
]
},
"generics": {
"Package": "generics",
"Version": "0.1.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "15e9634c0fcd294799e9b2e929ed1b86",
"Requirements": []
},
"ggplot2": {
"Package": "ggplot2",
"Version": "3.4.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "fd2aab12f54400c6bca43687231e246b",
"Requirements": [
"MASS",
"cli",
"glue",
"gtable",
"isoband",
"lifecycle",
"mgcv",
"rlang",
"scales",
"tibble",
"vctrs",
"withr"
]
},
"glue": {
"Package": "glue",
"Version": "1.6.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "4f2596dfb05dac67b9dc558e5c6fba2e",
"Requirements": []
},
"googledrive": {
"Package": "googledrive",
"Version": "2.0.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "c3a25adbbfbb03f12e6f88c5fb1f3024",
"Requirements": [
"cli",
"gargle",
"glue",
"httr",
"jsonlite",
"lifecycle",
"magrittr",
"pillar",
"purrr",
"rlang",
"tibble",
"uuid",
"vctrs",
"withr"
]
},
"googlesheets4": {
"Package": "googlesheets4",
"Version": "1.0.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "3b449d5292327880fc6cb61d0b2e9063",
"Requirements": [
"cellranger",
"cli",
"curl",
"gargle",
"glue",
"googledrive",
"httr",
"ids",
"magrittr",
"purrr",
"rematch2",
"rlang",
"tibble",
"vctrs"
]
},
"gtable": {
"Package": "gtable",
"Version": "0.3.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "36b4265fb818f6a342bed217549cd896",
"Requirements": []
},
"haven": {
"Package": "haven",
"Version": "2.5.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "5b45a553fca2217a07b6f9c843304c44",
"Requirements": [
"cli",
"cpp11",
"forcats",
"hms",
"lifecycle",
"readr",
"rlang",
"tibble",
"tidyselect",
"vctrs"
]
},
"here": {
"Package": "here",
"Version": "1.0.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "24b224366f9c2e7534d2344d10d59211",
"Requirements": [
"rprojroot"
]
},
"highr": {
"Package": "highr",
"Version": "0.10",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "06230136b2d2b9ba5805e1963fa6e890",
"Requirements": [
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]
},
"hms": {
"Package": "hms",
"Version": "1.1.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "41100392191e1244b887878b533eea91",
"Requirements": [
"ellipsis",
"lifecycle",
"pkgconfig",
"rlang",
"vctrs"
]
},
"htmltools": {
"Package": "htmltools",
"Version": "0.5.4",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "9d27e99cc90bd701c0a7a63e5923f9b7",
"Requirements": [
"base64enc",
"digest",
"ellipsis",
"fastmap",
"rlang"
]
},
"httr": {
"Package": "httr",
"Version": "1.4.4",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "57557fac46471f0dbbf44705cc6a5c8c",
"Requirements": [
"R6",
"curl",
"jsonlite",
"mime",
"openssl"
]
},
"ids": {
"Package": "ids",
"Version": "1.0.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "99df65cfef20e525ed38c3d2577f7190",
"Requirements": [
"openssl",
"uuid"
]
},
"isoband": {
"Package": "isoband",
"Version": "0.2.7",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "0080607b4a1a7b28979aecef976d8bc2",
"Requirements": []
},
"janitor": {
"Package": "janitor",
"Version": "2.1.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "6de84a8c67fb247e721166049c84695f",
"Requirements": [
"dplyr",
"lifecycle",
"lubridate",
"magrittr",
"purrr",
"rlang",
"snakecase",
"stringi",
"stringr",
"tidyr",
"tidyselect"
]
},
"jquerylib": {
"Package": "jquerylib",
"Version": "0.1.4",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "5aab57a3bd297eee1c1d862735972182",
"Requirements": [
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]
},
"jsonlite": {
"Package": "jsonlite",
"Version": "1.8.4",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "a4269a09a9b865579b2635c77e572374",
"Requirements": []
},
"knitr": {
"Package": "knitr",
"Version": "1.41",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "6d4971f3610e75220534a1befe81bc92",
"Requirements": [
"evaluate",
"highr",
"stringr",
"xfun",
"yaml"
]
},
"labeling": {
"Package": "labeling",
"Version": "0.4.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "3d5108641f47470611a32d0bdf357a72",
"Requirements": []
},
"lattice": {
"Package": "lattice",
"Version": "0.20-45",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b64cdbb2b340437c4ee047a1f4c4377b",
"Requirements": []
},
"lifecycle": {
"Package": "lifecycle",
"Version": "1.0.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "001cecbeac1cff9301bdc3775ee46a86",
"Requirements": [
"cli",
"glue",
"rlang"
]
},
"lubridate": {
"Package": "lubridate",
"Version": "1.9.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "2af4550c2f0f7fbe7cbbf3dbf4ea3902",
"Requirements": [
"generics",
"timechange"
]
},
"magrittr": {
"Package": "magrittr",
"Version": "2.0.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "7ce2733a9826b3aeb1775d56fd305472",
"Requirements": []
},
"memoise": {
"Package": "memoise",
"Version": "2.0.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c",
"Requirements": [
"cachem",
"rlang"
]
},
"mgcv": {
"Package": "mgcv",
"Version": "1.8-41",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6b3904f13346742caa3e82dd0303d4ad",
"Requirements": [
"Matrix",
"nlme"
]
},
"mime": {
"Package": "mime",
"Version": "0.12",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "18e9c28c1d3ca1560ce30658b22ce104",
"Requirements": []
},
"modelr": {
"Package": "modelr",
"Version": "0.1.10",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "bc23cda9c6a8f91dc1c10e1994494711",
"Requirements": [
"broom",
"magrittr",
"purrr",
"rlang",
"tibble",
"tidyr",
"tidyselect",
"vctrs"
]
},
"munsell": {
"Package": "munsell",
"Version": "0.5.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "6dfe8bf774944bd5595785e3229d8771",
"Requirements": [
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]
},
"nlme": {
"Package": "nlme",
"Version": "3.1-160",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "02e3c6e7df163aafa8477225e6827bc5",
"Requirements": [
"lattice"
]
},
"openssl": {
"Package": "openssl",
"Version": "2.0.5",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "b04c27110bf367b4daa93f34f3d58e75",
"Requirements": [
"askpass"
]
},
"pillar": {
"Package": "pillar",
"Version": "1.8.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "f2316df30902c81729ae9de95ad5a608",
"Requirements": [
"cli",
"fansi",
"glue",
"lifecycle",
"rlang",
"utf8",
"vctrs"
]
},
"pkgconfig": {
"Package": "pkgconfig",
"Version": "2.0.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "01f28d4278f15c76cddbea05899c5d6f",
"Requirements": []
},
"prettyunits": {
"Package": "prettyunits",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "95ef9167b75dde9d2ccc3c7528393e7e",
"Requirements": []
},
"processx": {
"Package": "processx",
"Version": "3.8.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "a33ee2d9bf07564efb888ad98410da84",
"Requirements": [
"R6",
"ps"
]
},
"progress": {
"Package": "progress",
"Version": "1.2.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "14dc9f7a3c91ebb14ec5bb9208a07061",
"Requirements": [
"R6",
"crayon",
"hms",
"prettyunits"
]
},
"ps": {
"Package": "ps",
"Version": "1.7.2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "68dd03d98a5efd1eb3012436de45ba83",
"Requirements": []
},
"purrr": {
"Package": "purrr",
"Version": "1.0.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "1ad491d27989ec6c26a2918ad6df116b",
"Requirements": [
"cli",
"lifecycle",
"magrittr",
"rlang",
"vctrs"
]
},
"rappdirs": {
"Package": "rappdirs",
"Version": "0.3.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "5e3c5dc0b071b21fa128676560dbe94d",
"Requirements": []
},
"readr": {
"Package": "readr",
"Version": "2.1.3",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "2dfbfc673ccb3de3d8836b4b3bd23d14",
"Requirements": [
"R6",
"cli",
"clipr",
"cpp11",
"crayon",
"hms",
"lifecycle",
"rlang",
"tibble",
"tzdb",
"vroom"
]
},
"readxl": {
"Package": "readxl",
"Version": "1.4.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "5c1fbc365ac0a3fe7728ac79108b8e64",
"Requirements": [
"cellranger",
"cpp11",
"progress",
"tibble"
]
},
"rematch": {
"Package": "rematch",
"Version": "1.0.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "c66b930d20bb6d858cd18e1cebcfae5c",
"Requirements": []
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"tibble"
]
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"Hash": "d66fe009d4c20b7ab1927eb405db9ee2",
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"cli",
"clipr",
"fs",
"glue",
"knitr",
"lifecycle",
"rlang",
"rmarkdown",
"rstudioapi",
"withr"
]
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"Package": "rlang",
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},
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"Source": "Repository",
"Repository": "RSPM",
"Hash": "4e29299e1f4c7eabb0b8365b338adf3c",
"Requirements": [
"bslib",
"evaluate",
"htmltools",
"jquerylib",
"jsonlite",
"knitr",
"stringr",
"tinytex",
"xfun",
"yaml"
]
},
"rprojroot": {
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"Package": "rstudioapi",
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"Hash": "690bd2acc42a9166ce34845884459320",
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},
"rvest": {
"Package": "rvest",
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"Requirements": [
"cli",
"glue",
"httr",
"lifecycle",
"magrittr",
"rlang",
"selectr",
"tibble",
"withr",
"xml2"
]
},
"sass": {
"Package": "sass",
"Version": "0.4.4",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "c76cbac7ca04ce82d8c38e29729987a3",
"Requirements": [
"R6",
"fs",
"htmltools",
"rappdirs",
"rlang"
]
},
"scales": {
"Package": "scales",
"Version": "1.2.1",
"Source": "Repository",
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"Hash": "906cb23d2f1c5680b8ce439b44c6fa63",
"Requirements": [
"R6",
"RColorBrewer",
"farver",
"labeling",
"lifecycle",
"munsell",
"rlang",
"viridisLite"
]
},
"selectr": {
"Package": "selectr",
"Version": "0.4-2",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "3838071b66e0c566d55cc26bd6e27bf4",
"Requirements": [
"R6",
"stringr"
]
},
"snakecase": {
"Package": "snakecase",
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"Source": "Repository",
"Repository": "RSPM",
"Hash": "4079070fc210c7901c0832a3aeab894f",
"Requirements": [
"stringi",
"stringr"
]
},
"stringi": {
"Package": "stringi",
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"Source": "Repository",
"Repository": "RSPM",
"Hash": "a68b980681bcbc84c7a67003fa796bfb",
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},
"stringr": {
"Package": "stringr",
"Version": "1.5.0",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "671a4d384ae9d32fc47a14e98bfa3dc8",
"Requirements": [
"cli",
"glue",
"lifecycle",
"magrittr",
"rlang",
"stringi",
"vctrs"
]
},
"sys": {
"Package": "sys",
"Version": "3.4.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "34c16f1ef796057bfa06d3f4ff818a5d",
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},
"tibble": {
"Package": "tibble",
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"Hash": "56b6934ef0f8c68225949a8672fe1a8f",
"Requirements": [
"fansi",
"lifecycle",
"magrittr",
"pillar",
"pkgconfig",
"rlang",
"vctrs"
]
},
"tidyr": {
"Package": "tidyr",
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"Source": "Repository",
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"dplyr",
"ellipsis",
"glue",
"lifecycle",
"magrittr",
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"vctrs"
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"tidyselect": {
"Package": "tidyselect",
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"Source": "Repository",
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"Hash": "79540e5fcd9e0435af547d885f184fd5",
"Requirements": [
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"lifecycle",
"rlang",
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"withr"
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},
"tidyverse": {
"Package": "tidyverse",
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"Source": "Repository",
"Repository": "RSPM",
"Hash": "972389aea7fa1a34739054a810d0c6f6",
"Requirements": [
"broom",
"cli",
"crayon",
"dbplyr",
"dplyr",
"dtplyr",
"forcats",
"ggplot2",
"googledrive",
"googlesheets4",
"haven",
"hms",
"httr",
"jsonlite",
"lubridate",
"magrittr",
"modelr",
"pillar",
"purrr",
"readr",
"readxl",
"reprex",
"rlang",
"rstudioapi",
"rvest",
"stringr",
"tibble",
"tidyr",
"xml2"
]
},
"timechange": {
"Package": "timechange",
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"tinytex": {
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"xfun"
]
},
"tzdb": {
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"Repository": "RSPM",
"Hash": "b2e1cbce7c903eaf23ec05c58e59fb5e",
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"utf8": {
"Package": "utf8",
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"Hash": "c9c462b759a5cc844ae25b5942654d13",
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"uuid": {
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"Repository": "RSPM",
"Hash": "f1cb46c157d080b729159d407be83496",
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"vctrs": {
"Package": "vctrs",
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"Source": "Repository",
"Repository": "RSPM",
"Hash": "970324f6572b4fd81db507b5d4062cb0",
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"glue",
"lifecycle",
"rlang"
]
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"Repository": "RSPM",
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"vroom": {
"Package": "vroom",
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"Source": "Repository",
"Repository": "RSPM",
"Hash": "64f81fdead6e0d250fb041e175d123ab",
"Requirements": [
"bit64",
"cli",
"cpp11",
"crayon",
"glue",
"hms",
"lifecycle",
"progress",
"rlang",
"tibble",
"tidyselect",
"tzdb",
"vctrs",
"withr"
]
},
"withr": {
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"Source": "Repository",
"Repository": "RSPM",
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"xfun": {
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}
}
}
But Dropbox might ruin…
(Advanced) renv with Cloud Storage
(Advanced) Docker
Problems renv can solve are only packages. They may come from differences in
- R versions ⇒ Always use the latest version of R
- Non-R dependencies (e.g., geospatial packages) ⇒ Docker can solve
- OS (only Windows binary produces bugs…) ⇒ Docker can solve
Docker
- A virtual machine. Write a blueprint (Dockerfile) including information of OS (Linux), Application (R and others), and Packages
- If you work on Docker, others can perfectly replicate your environment
Handson 1
- Clone (or download) the course repositiory
- Open the course project (
workshop-r-2022.Rproj) - Run
renv::restore()in R console - Confirm you can render sample notebooks without any problem
Warning
Please make sure if you are using the latest R version 4.2.2 (2022-10-31).
Cleaning Strategy
The Fundamental Theorem of Readability
Code should be written to minimize the time it would take for someone else to understand it.
For economists,
\[ \text{Code} := \arg\min_{c \in \mathcal{C}}\mathbb{E}_i[R_{i}(c)] \]
where
- \(\mathcal{C}\): Set of codes that work
- \(i\): A potential reader including yourself at a different time point
- \(R_{i}(c)\): Time taken by person \(i\) to understand code \(c\)
Naming
For readability, you need to name variables informatively and non-misleadingly
| 🙆 Good | 🙅 Bad | |
|---|---|---|
| Bool | is_female, has_kids | female, no_kids |
| Category | industry8, emp3 | industry, emp_status |
| Bins | age_bin5, wage_bin10 | age, wage |
Naming
For readability, you need to name variables informatively and non-misleadingly
| 🙆 Good | 🙅 Bad | |
|---|---|---|
| Bool | is_female, has_kids | female, no_kids |
| Category | industry8, emp3 | industry, emp_status |
| Bins | age_bin5, wage_bin10 | age, wage |
Boolean
is_*,has_*,should_*indicates the type boolean.- Starting with
not_*/no_*increases a step of recognition
Naming
For readability, you need to name variables informatively and non-misleadingly
| 🙆 Good | 🙅 Bad | |
|---|---|---|
| Bool | is_female, has_kids | female, no_kids |
| Category | industry8, emp3 | industry, emp_status |
| Bins | age_bin5, wage_bin10 | age, wage |
Categorical
- Attached number indicates if it is categorical and its number
Naming
For readability, you need to name variables informatively and non-misleadingly
| 🙆 Good | 🙅 Bad | |
|---|---|---|
| Bool | is_female, has_kids | female, no_kids |
| Category | industry8, emp3 | industry, emp_status |
| Bins | age_bin5, wage_bin10 | age, wage |
Bins of continuous variables
- Need to avoid the confusion with its continuous variable
- Attached number shows the width of the bin
Rename at Once
Rows: 42,547
Columns: 5
$ num_expediente <dbl> 2.022e+04, 2.022e+04, 2.022e+05, 2.022e+05, 2.022e+05, …
$ fecha <chr> "01/01/2022", "01/01/2022", "01/01/2022", "01/01/2022",…
$ hora <time> 01:30:00, 01:30:00, 00:30:00, 00:30:00, 00:30:00, 01:5…
$ localizacion <chr> "AVDA. ALBUFERA, 19", "AVDA. ALBUFERA, 19", "PLAZA. CAN…
$ numero <chr> "19", "19", "2", "2", "2", "53", "53", "728", "728", "+…Rows: 42,547
Columns: 5
$ id_1922 <dbl> 2.022e+04, 2.022e+04, 2.022e+05, 2.022e+05, 2.022e+05, 2.02…
$ date <chr> "01/01/2022", "01/01/2022", "01/01/2022", "01/01/2022", "01…
$ hms <time> 01:30:00, 01:30:00, 00:30:00, 00:30:00, 00:30:00, 01:50:00…
$ street <chr> "AVDA. ALBUFERA, 19", "AVDA. ALBUFERA, 19", "PLAZA. CANOVAS…
$ num_street <chr> "19", "19", "2", "2", "2", "53", "53", "728", "728", "+0050…| spanish | english |
|---|---|
| num_expediente | id_1922 |
| fecha | date |
| hora | hms |
| localizacion | street |
| numero | num_street |
| cod_distrito | code_district |
| distrito | district |
| tipo_accidente | type_accident |
| estado_meteorológico | weather |
| tipo_vehiculo | type_vehicle |
| tipo_persona | type_person |
| rango_edad | age_c |
| sexo | gender |
| cod_lesividad | code_injury8 |
| lesividad | injury8 |
| coordenada_x_utm | coord_x |
| coordenada_y_utm | coord_y |
| positiva_alcohol | positive_alcohol |
| positiva_droga | positive_drug |
Type
Facotrizing
Format: Parquet
(Advanced) Parquet with Large Dataset
Cleaning Workflow
Handson 2
Some example of cleaning
Tips in Plots
Layers in ggplots
Scales
Color Palette
Themes
Third-party Themes
My Favorite ggplot2 Family
Automated Table Creation
kableExtra: Example
# A tibble: 6 × 9
# Groups: weather [6]
weather n_men_2019 n_men_2…¹ n_men…² n_men…³ n_wom…⁴ n_wom…⁵ n_wom…⁶ n_wom…⁷
<fct> <int> <int> <int> <int> <int> <int> <int> <int>
1 sunny 24399 14969 19208 19420 11971 6958 9417 9298
2 cloud 1159 1190 1325 1633 555 554 630 774
3 soft rain 2126 1198 1281 1408 1068 542 605 716
4 hard rain 386 202 386 352 222 96 210 179
5 snow 2 2 124 5 NA NA 38 1
6 hail 11 5 6 4 3 3 1 2
# … with abbreviated variable names ¹n_men_2020, ²n_men_2021, ³n_men_2022,
# ⁴n_women_2019, ⁵n_women_2020, ⁶n_women_2021, ⁷n_women_2022library(kableExtra)
options(knitr.kable.NA = '')
ktb <- tab |>
kbl(format = "latex", booktabs = TRUE,
col.names = c(" ", 2019:2022, 2019:2022)) |>
add_header_above(c(" ", "Men" = 4, "Women" = 4)) |>
pack_rows(index = c("Good" = 2, "Bad" = 4))
ktb |>
save_kable(here("output/tex/kableextra/tb_accident_bike.tex"))
booktabs = TRUEforbooktabspackage in LaTeX- You can specify the column names by
col.names - You can pack columns and rows by
add_header_above()andpack_rows() save_kable()saves in a tex file if the file name ends with “.tex”
kableExtra
Dataframe (tibble) to Table
- Create a tibble table by
dplyr::group_by&dpyr::summarizeandjanitor::tabyl() - For regression tables, you can use
modelsummary(next slide)
Pack Columns and Rows
- As far as I know, Python, Julia, and Stata do not allow us to pack them easily
More Complicated Tables
- You can refer to Hao Zhu’s document
- If a table contains a mathematical expression, use
escape=FALSE. See a discussion in stacoverflow
modelsummary
Given the following regression results,
library(fixest) # for faster regression with fixed effect
models <- list(
"(1)" = feglm(is_hospitalized ~ type_person + positive_alcohol + positive_drug | age_c + gender,
family = binomial(logit), data = data),
"(2)" = feglm(is_hospitalized ~ type_person + positive_alcohol + positive_drug | age_c + gender + type_vehicle,
family = binomial(logit), data = data),
"(3)" = feglm(is_hospitalized ~ type_person + positive_alcohol + positive_drug | age_c + gender + type_vehicle + weather,
family = binomial(logit), data = data),
"(4)" = feglm(is_died ~ type_person + positive_alcohol + positive_drug | age_c + gender,
family = binomial(logit), data = data),
"(5)" = feglm(is_died ~ type_person + positive_alcohol + positive_drug | age_c + gender + type_vehicle,
family = binomial(logit), data = data),
"(6)" = feglm(is_died ~ type_person + positive_alcohol + positive_drug | age_c + gender + type_vehicle + weather,
family = binomial(logit), data = data)
)modelsummary: Init
| (1) | (2) | (3) | (4) | (5) | (6) | |
|---|---|---|---|---|---|---|
| type_personpassenger | 0.049 | 0.530 | 0.507 | −1.781 | −1.575 | −1.565 |
| (0.104) | (0.071) | (0.070) | (0.759) | (0.783) | (0.784) | |
| type_personpedestrian | 2.124 | 2.402 | 2.323 | 2.280 | 2.418 | 2.422 |
| (0.115) | (0.066) | (0.064) | (0.301) | (0.287) | (0.285) | |
| positive_alcoholTRUE | −0.077 | 0.310 | 0.353 | −13.710 | −13.455 | −13.492 |
| (0.088) | (0.095) | (0.093) | (0.053) | (0.064) | (0.063) | |
| Num.Obs. | 149918 | 149831 | 134006 | 90852 | 89300 | 86330 |
| R2 | 0.055 | 0.171 | 0.165 | 0.107 | 0.145 | 0.148 |
| R2 Adj. | 0.054 | 0.170 | 0.163 | 0.086 | 0.113 | 0.112 |
| R2 Within | 0.047 | 0.054 | 0.052 | 0.073 | 0.076 | 0.076 |
| R2 Within Adj. | 0.047 | 0.054 | 0.052 | 0.070 | 0.072 | 0.073 |
| AIC | 62871.0 | 55210.6 | 53565.4 | 1601.9 | 1552.2 | 1534.5 |
| BIC | 63079.3 | 55696.5 | 54085.1 | 1780.8 | 1824.8 | 1834.2 |
| RMSE | 0.23 | 0.22 | 0.23 | 0.04 | 0.04 | 0.04 |
| Std.Errors | by: age_c | by: age_c | by: age_c | by: age_c | by: age_c | by: age_c |
| FE: age_c | X | X | X | X | X | X |
| FE: gender | X | X | X | X | X | X |
| FE: type_vehicle | X | X | X | X | ||
| FE: weather | X | X |
modelsummary: Modify Coefficients
| (1) | (2) | (3) | (4) | (5) | (6) | |
|---|---|---|---|---|---|---|
| Passenger | 0.049 | 0.530 | 0.507 | −1.781 | −1.575 | −1.565 |
| (0.104) | (0.071) | (0.070) | (0.759) | (0.783) | (0.784) | |
| Pedestrian | 2.124 | 2.402 | 2.323 | 2.280 | 2.418 | 2.422 |
| (0.115) | (0.066) | (0.064) | (0.301) | (0.287) | (0.285) | |
| Positive Alcohol | −0.077 | 0.310 | 0.353 | −13.710 | −13.455 | −13.492 |
| (0.088) | (0.095) | (0.093) | (0.053) | (0.064) | (0.063) | |
| Num.Obs. | 149918 | 149831 | 134006 | 90852 | 89300 | 86330 |
| R2 | 0.055 | 0.171 | 0.165 | 0.107 | 0.145 | 0.148 |
| R2 Adj. | 0.054 | 0.170 | 0.163 | 0.086 | 0.113 | 0.112 |
| R2 Within | 0.047 | 0.054 | 0.052 | 0.073 | 0.076 | 0.076 |
| R2 Within Adj. | 0.047 | 0.054 | 0.052 | 0.070 | 0.072 | 0.073 |
| AIC | 62871.0 | 55210.6 | 53565.4 | 1601.9 | 1552.2 | 1534.5 |
| BIC | 63079.3 | 55696.5 | 54085.1 | 1780.8 | 1824.8 | 1834.2 |
| RMSE | 0.23 | 0.22 | 0.23 | 0.04 | 0.04 | 0.04 |
| Std.Errors | by: age_c | by: age_c | by: age_c | by: age_c | by: age_c | by: age_c |
| FE: age_c | X | X | X | X | X | X |
| FE: gender | X | X | X | X | X | X |
| FE: type_vehicle | X | X | X | X | ||
| FE: weather | X | X |
modelsummary: Modify Statitics
cm <- c(
"type_personpassenger" = "Passenger",
"type_personpedestrian" = "Pedestrian",
"positive_alcoholTRUE" = "Positive Alcohol"
)
gm <- tibble(
raw = c("nobs", "FE: age_c", "FE: gender", "FE: type_vehicle", "FE: weather"),
clean = c("Observations", "FE: Age Group", "FE: Gender", "FE: Type of Vehicle", "FE: Weather"),
fmt = c(0, 0, 0, 0, 0)
)
modelsummary(models,
coef_map = cm,
gof_map = gm
)| (1) | (2) | (3) | (4) | (5) | (6) | |
|---|---|---|---|---|---|---|
| Passenger | 0.049 | 0.530 | 0.507 | −1.781 | −1.575 | −1.565 |
| (0.104) | (0.071) | (0.070) | (0.759) | (0.783) | (0.784) | |
| Pedestrian | 2.124 | 2.402 | 2.323 | 2.280 | 2.418 | 2.422 |
| (0.115) | (0.066) | (0.064) | (0.301) | (0.287) | (0.285) | |
| Positive Alcohol | −0.077 | 0.310 | 0.353 | −13.710 | −13.455 | −13.492 |
| (0.088) | (0.095) | (0.093) | (0.053) | (0.064) | (0.063) | |
| Observations | 149918 | 149831 | 134006 | 90852 | 89300 | 86330 |
| FE: Age Group | X | X | X | X | X | X |
| FE: Gender | X | X | X | X | X | X |
| FE: Type of Vehicle | X | X | X | X | ||
| FE: Weather | X | X |
modelsummary: Decorate
cm <- c(
"type_personpassenger" = "Passenger",
"type_personpedestrian" = "Pedestrian",
"positive_alcoholTRUE" = "Positive Alcohol"
)
gm <- tibble(
raw = c("nobs", "FE: age_c", "FE: gender", "FE: type_vehicle", "FE: weather"),
clean = c("Observations", "FE: Age Group", "FE: Gender", "FE: Type of Vehicle", "FE: Weather"),
fmt = c(0, 0, 0, 0, 0)
)
modelsummary(models,
stars = c("+" = .1, "*" = .05, "**" = .01),
coef_map = cm,
gof_map = gm) |>
add_header_above(c(" ", "Hospitalization" = 3, "Died within 24 hours" = 3)) Hospitalization |
Died within 24 hours |
|||||
|---|---|---|---|---|---|---|
| (1) | (2) | (3) | (4) | (5) | (6) | |
| Passenger | 0.049 | 0.530** | 0.507** | −1.781* | −1.575+ | −1.565+ |
| (0.104) | (0.071) | (0.070) | (0.759) | (0.783) | (0.784) | |
| Pedestrian | 2.124** | 2.402** | 2.323** | 2.280** | 2.418** | 2.422** |
| (0.115) | (0.066) | (0.064) | (0.301) | (0.287) | (0.285) | |
| Positive Alcohol | −0.077 | 0.310** | 0.353** | −13.710** | −13.455** | −13.492** |
| (0.088) | (0.095) | (0.093) | (0.053) | (0.064) | (0.063) | |
| Observations | 149918 | 149831 | 134006 | 90852 | 89300 | 86330 |
| FE: Age Group | X | X | X | X | X | X |
| FE: Gender | X | X | X | X | X | X |
| FE: Type of Vehicle | X | X | X | X | ||
| FE: Weather | X | X | ||||
| + p < 0.1, * p < 0.05, ** p < 0.01 | ||||||
modelsummary: Export to \(\LaTeX\)
cm <- c(
"type_personpassenger" = "Passenger",
"type_personpedestrian" = "Pedestrian",
"positive_alcoholTRUE" = "Positive Alcohol"
)
gm <- tibble(
raw = c("nobs", "FE: age_c", "FE: gender", "FE: type_vehicle", "FE: weather"),
clean = c("Observations", "FE: Age Group", "FE: Gender", "FE: Type of Vehicle", "FE: Weather"),
fmt = c(0, 0, 0, 0, 0)
)
modelsummary(models,
output = "latex_tabular",
stars = c("+" = .1, "*" = .05, "**" = .01),
coef_map = cm,
gof_map = gm) |>
add_header_above(c(" ", "Hospitalization" = 3, "Died within 24 hours" = 3)) |>
row_spec(7, hline_after = T) |>
save_kable(here("output/tex/modelsummary/reg_accident_bike.tex"))